AMBER Archive (2002)

Subject: FEP/Gibbs question

From: meiselba (Heike.Meiselbach_at_organik.uni-erlangen.de)
Date: Tue Nov 19 2002 - 09:29:07 CST

Hello,
I have two questions regarding gibbs (Amber 5).
My first question:
I am working with the "Simple free energy example" tutorial in the web.
When I try to perform a valine to alanine free energy determination with
Gibbs as the
tutorial describes, I get an error in Xleap. The error message is: Could
not find the perturbed type DH and Parameter file was not saved.
What am I doing wrong?
My second question:
I would like to simulate free energy perturbation with a mutation of
tetracycline to anhydrotetracycline.
How can I create a gibbs input file for the mutation of tetracycline to
anhydrotetracycline and how can I vary the charges? What are the dummy
atoms?

Thanks in advance!
Heike Meiselbach

Computer-Chemie-Centrum,
Friedrich-Alexander-Universitaet Erlangen-Nuernberg
Naegelsbachstraße 25
D-91052 Erlangen

Tel. +49 9131 85-26534
Fax +49 9131 85-26565